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I have to study a given quite large ontology represented with a triple store, to understand what kind of content is represented and how it's organized. I'm working with Protege 5.2.0 on a Windows 10 machine equipped with a Intel Core i7-6500U and 8 GB of RAM.

The main trouble reside on the heavyness of the triple store ( more or less 200 MB) that cause trouble on the ontology loading process in Protege and the management of ontology on the program itself.

I suceeded to solve the problem regarding the loading process increasing the avalaible memory for the JVM from 466 MB to 4 GB and single thread memory from 16 MB to 2 GB.

However, once the loading was successfully completed (as shown in the log file),even after a long time (more than 20 minutes) Protege results unusable because of the heavyness of the process. However, with a lot of effort, I succeeded to reach the Entity tab and I saw that, according to Protege, no entity,class or individual exists, but only annotations. In the log file, there's no error reported, but for each line a warning like

2017-05-12 14:54:54.937 [pool-2-thread-1] WARN  OBOFormatParser    LINE: 31 Expected white space at pos: 6  LINE:<http://minerva.atcult.it/rdf/000000362375> <http://purl.org/ontology/bibo/numPages> "14 p" .

Is the problem related to the triple store,or can it be solved using a particular plugin/setting on Protege?

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  • Annotations can exist on axioms, entities and anonymous individuals. If you're not seeing entities, the ontology might contain only assertions about individuals and annotation properties for annotating them. This might depend on a number of things, including errors in the ontology itself - but these cannot be figured out from what you've described. Is the ontology public? – Ignazio May 13 '17 at 22:49

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As suggested in comment, I looked for errors in the ontology and I found one. In fact, the ontology couldn't be loaded because of a white space on a row of the nt file. Now it works, and Protegé loads the ontology correctly.

Jul10
  • 503
  • 7
  • 19